Fluorescent proteins (FPs) constitute major research tools for the dissection of biological pathways at the cellular, subcellular, and molecular levels. The green fluorescent protein (GFP) from the jellyfish Aequorea victoria was the first fluorescent protein to be fully characterized and used. GFP rapidly became a major tool in molecular and cellular biology because it is naturally and spontaneously fluorescent and it can be fused to other proteins. This made GFP a biomarker of choice for a wide range of in vivo and in vitro applications. Following the initial discovery of A. victoria GFP, intensive research effort has resulted in the discovery, characterization and development of homologous fluorescent proteins with a wide range of optical and chemical properties. Fluorescent proteins from various species, including Arthropoda, Hydrozoa, and Anthozoa species, have now been characterized and several of their properties determine their usage. There is a present need to identify, modify, and optimize additional fluorescent proteins with characteristics that serve as novel and more efficient markers for in vivo and in vitro molecular imaging.